proteomics 0.3.8__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- proteomics-0.3.8/.gitignore +62 -0
- proteomics-0.3.8/CHANGELOG.md +22 -0
- proteomics-0.3.8/LICENSE +1 -0
- proteomics-0.3.8/NOTICE +1 -0
- proteomics-0.3.8/PKG-INFO +195 -0
- proteomics-0.3.8/README.md +162 -0
- proteomics-0.3.8/pyproject.toml +63 -0
- proteomics-0.3.8/src/proteomics/py.typed +1 -0
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# Changelog
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All notable changes for `proteomics` are recorded here.
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## Unreleased
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## 0.3.8 - 2026-07-01
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### Added
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- Added the `proteomics` distribution as the short install, import, and CLI
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alias for `bijux-proteomics-core`.
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- Added explicit alias-package contract and README guidance so the short name
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still routes readers and imports to the canonical core owner.
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### Changed
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- Aligned the fallback version and canonical dependency floors with the
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`0.3.8` release line.
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- Routed short-name compatibility through governed foundation helpers, lazy
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imports, and clean-checkout alias verification instead of durable shim
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modules.
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proteomics-0.3.8/LICENSE
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../../LICENSE
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proteomics-0.3.8/NOTICE
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../../NOTICE
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Metadata-Version: 2.4
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Name: proteomics
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Version: 0.3.8
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Summary: Install, import, and CLI alias package for bijux-proteomics-core.
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Project-URL: Homepage, https://bijux.io/bijux-proteomics/
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Project-URL: Documentation, https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/
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Project-URL: Repository, https://github.com/bijux/bijux-proteomics
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Project-URL: Issues, https://github.com/bijux/bijux-proteomics/issues
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Project-URL: Changelog, https://github.com/bijux/bijux-proteomics/blob/main/packages/proteomics/CHANGELOG.md
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Project-URL: Security, https://github.com/bijux/bijux-proteomics/blob/main/SECURITY.md
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Author-email: Bijan Mousavi <bijan@bijux.io>
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Maintainer-email: Bijan Mousavi <bijan@bijux.io>
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License: Apache-2.0
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License-File: LICENSE
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License-File: NOTICE
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Keywords: bioinformatics,compatibility,packaging,proteomics
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Classifier: Development Status :: 3 - Alpha
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Classifier: Intended Audience :: Developers
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Classifier: Intended Audience :: Science/Research
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Classifier: License :: OSI Approved :: Apache Software License
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Classifier: Operating System :: OS Independent
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3 :: Only
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: 3.13
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Classifier: Programming Language :: Python :: 3.14
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Classifier: Typing :: Typed
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Requires-Python: <4,>=3.11
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Requires-Dist: bijux-proteomics-core<0.4.0,>=0.3.8
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Requires-Dist: bijux-proteomics-foundation<0.4.0,>=0.3.8
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Description-Content-Type: text/markdown
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# proteomics
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<!-- bijux-proteomics-badges:generated:start -->
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[](https://pypi.org/project/proteomics/)
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[-0A7BBB)](https://pypi.org/project/proteomics/)
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[](https://github.com/bijux/bijux-proteomics/blob/main/LICENSE)
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[](https://github.com/bijux/bijux-proteomics/actions/workflows/verify.yml?query=branch%3Amain)
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[](https://github.com/bijux/bijux-proteomics)
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[](https://pypi.org/project/proteomics/)
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[](https://pypi.org/project/agentic-proteins/)
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[](https://pypi.org/project/bijux-proteomics-foundation/)
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[](https://pypi.org/project/bijux-proteomics-core/)
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[](https://pypi.org/project/bijux-proteomics-runtime/)
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[](https://pypi.org/project/bijux-proteomics-intelligence/)
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[](https://pypi.org/project/bijux-proteomics-knowledge/)
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[](https://pypi.org/project/bijux-proteomics-lab/)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fagentic-proteins)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-foundation)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-core)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-intelligence)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-knowledge)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-lab)
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[](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
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[](https://bijux.io/bijux-proteomics/02-agentic-proteins/)
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[](https://bijux.io/bijux-proteomics/03-bijux-proteomics-foundation/)
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[](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
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[](https://bijux.io/bijux-proteomics/09-bijux-proteomics-runtime/)
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[](https://bijux.io/bijux-proteomics/05-bijux-proteomics-intelligence/)
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[](https://bijux.io/bijux-proteomics/06-bijux-proteomics-knowledge/)
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[](https://bijux.io/bijux-proteomics/07-bijux-proteomics-lab/)
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<!-- bijux-proteomics-badges:generated:end -->
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`proteomics` is the short-name compatibility alias for the canonical core owner
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`bijux-proteomics-core`.
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It is the install and import alias for bijux-proteomics-core.
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Use this package when you want the shortest public distribution and import name
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for the core scientific surface without creating a second owner.
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## Alias at a glance
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- Use `proteomics` when the shortest install and import name matters more than
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the canonical owner package spelling.
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- Start behavior discovery from the
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[canonical core package docs](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
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because this package is only a short-name forwarding layer.
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- Route all scientific behavior to `bijux-proteomics-core`; keep this package
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focused on compatibility naming and short-form ergonomics.
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## 0.3.8 Release Highlights
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- The short-name alias now points readers straight at the current core docs
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and shipped scientific examples instead of reading like a second owner.
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- Compatibility wording, package boundaries, and release guidance now state
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directly that `bijux-proteomics-core` owns all real behavior.
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## Installation
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```bash
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pip install proteomics
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```
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## Public APIs
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The alias forwards to the canonical core surface through the short import root:
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```python
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from proteomics import parse_fasta_document
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report = parse_fasta_document(">sp|P11111|PTM1 Protein 1\nMPEPTIDEK\n")
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assert report.total_records == 1
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assert len(report.accepted_records) == 1
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assert report.accepted_records[0].canonical_accession == "P11111"
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```
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## Package identity
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- Distribution name: `proteomics`
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- Import root: `proteomics`
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- Canonical owner package: `bijux-proteomics-core`
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- Canonical owner import root: `bijux_proteomics`
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## Package boundaries
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- this package owns compatibility naming for installs, imports, and the short
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CLI surface
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- all scientific behavior remains owned by `bijux-proteomics-core`
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- new features must land in the canonical owner before alias exports change
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## What this package must not do
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- define independent scientific or workflow behavior
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- diverge from canonical core exports
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- become a second place where core release policy is decided
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## Contract checkpoints
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- the short import surface must keep forwarding to canonical core behavior
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- docs must continue to name `bijux-proteomics-core` as the owner
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- compatibility updates must stay covered by alias-package tests
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## Choose this package when
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- you need the shortest import and install name for the core surface
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- migration or user ergonomics favor `proteomics` over the canonical package
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name
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- compatibility packaging work needs a clear short-name alias
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## Route elsewhere when
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- the change alters core scientific logic or workflow semantics
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- the work adds a feature that is not already owned by core
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- the proposal would make the alias more than a forwarding layer
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## Verification route
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- run alias compatibility tests before changing imports or console-script
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expectations
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- review `docs/ARCHITECTURE.md`, `docs/BOUNDARIES.md`, and `docs/CONTRACTS.md`
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when alias claims or routing language change
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- validate the canonical core README and tests when the proposal changes
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user-facing scientific behavior
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## Review questions
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- does the change preserve this package as a short-name alias only
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- is the canonical owner explicit in behavior and documentation
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- would the same behavior remain valid if core were imported directly
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## Escalation route
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- route scientific behavior changes to `bijux-proteomics-core`
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- stop and review alias boundaries when the proposal introduces package-local
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semantics
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- escalate before release when packaging or command-name drift could confuse
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consumers
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## Consumer impact signals
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- short-name install or import changes are high-impact because downstream code
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may rely on them directly
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- alias documentation changes should still be reviewed against the core owner
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- wording-only or documentation-only clarifications carry lower release risk
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## Explicit non-goals
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- this package does not own assay-processing or workflow semantics
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- this package does not define runtime, intelligence, knowledge, or lab policy
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- this package does not replace the canonical core release surface
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## Documentation
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- Release guidance lives in this `README.md`, this package `CHANGELOG.md`, and
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package `docs/*.md` under the canonical core owner surface.
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- [Product architecture](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/product-architecture/)
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- [Cross-package ownership](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/cross-package-ownership/)
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- [Canonical core package docs](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
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- [Changelog](CHANGELOG.md)
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# proteomics
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<!-- bijux-proteomics-badges:generated:start -->
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[](https://pypi.org/project/proteomics/)
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[-0A7BBB)](https://pypi.org/project/proteomics/)
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[](https://github.com/bijux/bijux-proteomics/blob/main/LICENSE)
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[](https://github.com/bijux/bijux-proteomics/actions/workflows/verify.yml?query=branch%3Amain)
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[](https://github.com/bijux/bijux-proteomics)
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[](https://pypi.org/project/proteomics/)
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[](https://pypi.org/project/agentic-proteins/)
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[](https://pypi.org/project/bijux-proteomics-foundation/)
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[](https://pypi.org/project/bijux-proteomics-core/)
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[](https://pypi.org/project/bijux-proteomics-runtime/)
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[](https://pypi.org/project/bijux-proteomics-intelligence/)
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[](https://pypi.org/project/bijux-proteomics-knowledge/)
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[](https://pypi.org/project/bijux-proteomics-lab/)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fagentic-proteins)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-foundation)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-core)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-intelligence)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-knowledge)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-lab)
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[](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
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[](https://bijux.io/bijux-proteomics/02-agentic-proteins/)
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[](https://bijux.io/bijux-proteomics/03-bijux-proteomics-foundation/)
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[](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
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[](https://bijux.io/bijux-proteomics/09-bijux-proteomics-runtime/)
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[](https://bijux.io/bijux-proteomics/05-bijux-proteomics-intelligence/)
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[](https://bijux.io/bijux-proteomics/06-bijux-proteomics-knowledge/)
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[](https://bijux.io/bijux-proteomics/07-bijux-proteomics-lab/)
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<!-- bijux-proteomics-badges:generated:end -->
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`proteomics` is the short-name compatibility alias for the canonical core owner
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`bijux-proteomics-core`.
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It is the install and import alias for bijux-proteomics-core.
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Use this package when you want the shortest public distribution and import name
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for the core scientific surface without creating a second owner.
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## Alias at a glance
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- Use `proteomics` when the shortest install and import name matters more than
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the canonical owner package spelling.
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- Start behavior discovery from the
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[canonical core package docs](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
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because this package is only a short-name forwarding layer.
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- Route all scientific behavior to `bijux-proteomics-core`; keep this package
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focused on compatibility naming and short-form ergonomics.
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## 0.3.8 Release Highlights
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- The short-name alias now points readers straight at the current core docs
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and shipped scientific examples instead of reading like a second owner.
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- Compatibility wording, package boundaries, and release guidance now state
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directly that `bijux-proteomics-core` owns all real behavior.
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## Installation
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```bash
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pip install proteomics
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```
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## Public APIs
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The alias forwards to the canonical core surface through the short import root:
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```python
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from proteomics import parse_fasta_document
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report = parse_fasta_document(">sp|P11111|PTM1 Protein 1\nMPEPTIDEK\n")
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assert report.total_records == 1
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assert len(report.accepted_records) == 1
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assert report.accepted_records[0].canonical_accession == "P11111"
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```
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## Package identity
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- Distribution name: `proteomics`
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- Import root: `proteomics`
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- Canonical owner package: `bijux-proteomics-core`
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- Canonical owner import root: `bijux_proteomics`
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+
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## Package boundaries
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+
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- this package owns compatibility naming for installs, imports, and the short
|
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+
CLI surface
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- all scientific behavior remains owned by `bijux-proteomics-core`
|
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+
- new features must land in the canonical owner before alias exports change
|
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+
|
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+
## What this package must not do
|
|
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|
+
|
|
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|
+
- define independent scientific or workflow behavior
|
|
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+
- diverge from canonical core exports
|
|
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|
+
- become a second place where core release policy is decided
|
|
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|
+
|
|
100
|
+
## Contract checkpoints
|
|
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|
+
|
|
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|
+
- the short import surface must keep forwarding to canonical core behavior
|
|
103
|
+
- docs must continue to name `bijux-proteomics-core` as the owner
|
|
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|
+
- compatibility updates must stay covered by alias-package tests
|
|
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|
+
|
|
106
|
+
## Choose this package when
|
|
107
|
+
|
|
108
|
+
- you need the shortest import and install name for the core surface
|
|
109
|
+
- migration or user ergonomics favor `proteomics` over the canonical package
|
|
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|
+
name
|
|
111
|
+
- compatibility packaging work needs a clear short-name alias
|
|
112
|
+
|
|
113
|
+
## Route elsewhere when
|
|
114
|
+
|
|
115
|
+
- the change alters core scientific logic or workflow semantics
|
|
116
|
+
- the work adds a feature that is not already owned by core
|
|
117
|
+
- the proposal would make the alias more than a forwarding layer
|
|
118
|
+
|
|
119
|
+
## Verification route
|
|
120
|
+
|
|
121
|
+
- run alias compatibility tests before changing imports or console-script
|
|
122
|
+
expectations
|
|
123
|
+
- review `docs/ARCHITECTURE.md`, `docs/BOUNDARIES.md`, and `docs/CONTRACTS.md`
|
|
124
|
+
when alias claims or routing language change
|
|
125
|
+
- validate the canonical core README and tests when the proposal changes
|
|
126
|
+
user-facing scientific behavior
|
|
127
|
+
|
|
128
|
+
## Review questions
|
|
129
|
+
|
|
130
|
+
- does the change preserve this package as a short-name alias only
|
|
131
|
+
- is the canonical owner explicit in behavior and documentation
|
|
132
|
+
- would the same behavior remain valid if core were imported directly
|
|
133
|
+
|
|
134
|
+
## Escalation route
|
|
135
|
+
|
|
136
|
+
- route scientific behavior changes to `bijux-proteomics-core`
|
|
137
|
+
- stop and review alias boundaries when the proposal introduces package-local
|
|
138
|
+
semantics
|
|
139
|
+
- escalate before release when packaging or command-name drift could confuse
|
|
140
|
+
consumers
|
|
141
|
+
|
|
142
|
+
## Consumer impact signals
|
|
143
|
+
|
|
144
|
+
- short-name install or import changes are high-impact because downstream code
|
|
145
|
+
may rely on them directly
|
|
146
|
+
- alias documentation changes should still be reviewed against the core owner
|
|
147
|
+
- wording-only or documentation-only clarifications carry lower release risk
|
|
148
|
+
|
|
149
|
+
## Explicit non-goals
|
|
150
|
+
|
|
151
|
+
- this package does not own assay-processing or workflow semantics
|
|
152
|
+
- this package does not define runtime, intelligence, knowledge, or lab policy
|
|
153
|
+
- this package does not replace the canonical core release surface
|
|
154
|
+
|
|
155
|
+
## Documentation
|
|
156
|
+
|
|
157
|
+
- Release guidance lives in this `README.md`, this package `CHANGELOG.md`, and
|
|
158
|
+
package `docs/*.md` under the canonical core owner surface.
|
|
159
|
+
- [Product architecture](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/product-architecture/)
|
|
160
|
+
- [Cross-package ownership](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/cross-package-ownership/)
|
|
161
|
+
- [Canonical core package docs](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
|
|
162
|
+
- [Changelog](CHANGELOG.md)
|
|
@@ -0,0 +1,63 @@
|
|
|
1
|
+
[build-system]
|
|
2
|
+
requires = ["hatchling>=1.27.0,<1.31", "hatch-vcs>=0.4.0,<1.0"]
|
|
3
|
+
build-backend = "hatchling.build"
|
|
4
|
+
|
|
5
|
+
[project]
|
|
6
|
+
name = "proteomics"
|
|
7
|
+
dynamic = ["version"]
|
|
8
|
+
description = "Install, import, and CLI alias package for bijux-proteomics-core."
|
|
9
|
+
readme = "README.md"
|
|
10
|
+
license = { text = "Apache-2.0" }
|
|
11
|
+
requires-python = ">=3.11,<4"
|
|
12
|
+
authors = [{ name = "Bijan Mousavi", email = "bijan@bijux.io" }]
|
|
13
|
+
maintainers = [{ name = "Bijan Mousavi", email = "bijan@bijux.io" }]
|
|
14
|
+
keywords = ["proteomics", "bioinformatics", "compatibility", "packaging"]
|
|
15
|
+
classifiers = [
|
|
16
|
+
"Development Status :: 3 - Alpha",
|
|
17
|
+
"Intended Audience :: Science/Research",
|
|
18
|
+
"Intended Audience :: Developers",
|
|
19
|
+
"License :: OSI Approved :: Apache Software License",
|
|
20
|
+
"Operating System :: OS Independent",
|
|
21
|
+
"Programming Language :: Python :: 3",
|
|
22
|
+
"Programming Language :: Python :: 3 :: Only",
|
|
23
|
+
"Programming Language :: Python :: 3.11",
|
|
24
|
+
"Programming Language :: Python :: 3.12",
|
|
25
|
+
"Programming Language :: Python :: 3.13",
|
|
26
|
+
"Programming Language :: Python :: 3.14",
|
|
27
|
+
"Typing :: Typed",
|
|
28
|
+
]
|
|
29
|
+
dependencies = [
|
|
30
|
+
"bijux-proteomics-foundation>=0.3.8,<0.4.0",
|
|
31
|
+
"bijux-proteomics-core>=0.3.8,<0.4.0",
|
|
32
|
+
]
|
|
33
|
+
|
|
34
|
+
[project.urls]
|
|
35
|
+
Homepage = "https://bijux.io/bijux-proteomics/"
|
|
36
|
+
Documentation = "https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/"
|
|
37
|
+
Repository = "https://github.com/bijux/bijux-proteomics"
|
|
38
|
+
Issues = "https://github.com/bijux/bijux-proteomics/issues"
|
|
39
|
+
Changelog = "https://github.com/bijux/bijux-proteomics/blob/main/packages/proteomics/CHANGELOG.md"
|
|
40
|
+
Security = "https://github.com/bijux/bijux-proteomics/blob/main/SECURITY.md"
|
|
41
|
+
|
|
42
|
+
[project.scripts]
|
|
43
|
+
proteomics = "proteomics.cli:main"
|
|
44
|
+
|
|
45
|
+
[tool.hatch.version]
|
|
46
|
+
source = "vcs"
|
|
47
|
+
tag-pattern = "^v(?P<version>.*)$"
|
|
48
|
+
fallback-version = "0.3.8"
|
|
49
|
+
raw-options = { git_describe_command = "git describe --dirty --tags --long --match 'v*'", local_scheme = "dirty-tag", version_scheme = "guess-next-dev", root = "../..", search_parent_directories = true }
|
|
50
|
+
|
|
51
|
+
[tool.hatch.build]
|
|
52
|
+
include = [
|
|
53
|
+
"README.md",
|
|
54
|
+
"CHANGELOG.md",
|
|
55
|
+
"src/proteomics/py.typed",
|
|
56
|
+
]
|
|
57
|
+
force-include = { "LICENSE" = "LICENSE", "NOTICE" = "NOTICE" }
|
|
58
|
+
|
|
59
|
+
[tool.hatch.build.targets.wheel]
|
|
60
|
+
packages = ["src/proteomics"]
|
|
61
|
+
|
|
62
|
+
[tool.hatch.build.targets.wheel.package-data]
|
|
63
|
+
"proteomics" = ["py.typed"]
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
|